Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis.
2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more appropriate
to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness is
15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more appropriate
to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness is
15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
There is not a difference between mris_fwhm and mri_surf2surf. mris_smooth smoothes the xyz coordinates of the vertices of a surface (the others smooth an overlay).
On 05/05/2016 03:53 PM, Ajay Kurani wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values). I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness. Thanks, Ajay On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files.
mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf?
2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial?
Best, Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more appropriate
to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness
is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used?
Thanks, Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files.
mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
- For cortical thickness does it make sense to use the --cortex option or
should I specify a mask of some type (if so which) in mris_surf2surf?
- For converting files to .gii should I be using rh.white as the option
or should it be rh.pial?
Best, Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more
appropriate to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness
is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
It estimates the FWHM from the data (glmdir/fwhm.dat). It does this by computing the pearson correation coefficient of the residual error between adjacent vertices. This is then averaged over all vertices to compute a mean cor coef. A transform is then applied to compute the FWHM. This is consistent in that if you synthesize white gaussian noise on the surface, then smooth it with a given FWHM (mri_surf2surf or mris_fwhm), then use that data to compute the FWHM, the applied and estimated FWHM will be equal (or close).
If you look in a given file produced by the simulator, eg, $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs/th20/mc-z.cdf the two relevant columns will be MaxClustBin and MaxClustCDF, eg, # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDF MaxSigBin MaxSigPDF MaxSigCDF 33 181.572128 0.010100 0.092500 0.132425 14.427808 0.004600 0.593700 Means that a cluster of size 181.57 has a probability of 0.0925 under the null when the FWHM=10 and the threshold is p<.01 (th20)
On 05/06/2016 03:59 PM, Ajay Kurani wrote:
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used?
Thanks, Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth. For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files. mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii 1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf? 2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial? Best, Ajay On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Doug, Thanks for the quick reply. Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis? Thanks, Ajay On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values). I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness. Thanks, Ajay On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify.
Thanks, Ajay
Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo
On Friday, May 6, 2016, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used?
Thanks, Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files.
mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
- For cortical thickness does it make sense to use the --cortex option
or should I specify a mask of some type (if so which) in mris_surf2surf?
- For converting files to .gii should I be using rh.white as the option
or should it be rh.pial?
Best, Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more
appropriate to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness
is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
Also is there a T/Z threshold applied? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?.
Thanks, Ajay
On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify.
Thanks, Ajay
Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo
On Friday, May 6, 2016, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used?
Thanks, Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files.
mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
- For cortical thickness does it make sense to use the --cortex option
or should I specify a mask of some type (if so which) in mris_surf2surf?
- For converting files to .gii should I be using rh.white as the option
or should it be rh.pial?
Best, Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more
appropriate to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the
smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
On 05/09/2016 04:11 PM, Ajay Kurani wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
It is the overall alpha, but the test is unsigned, so it is 5% for |A-B|>0
Also is there a T/Z threshold applied? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?.
In the simulation, the cluster-forming threshold (eg, p<.01,sig>2) is converted into a z-score and used to threshold the smoothed z-map. No t-thresholding is done,.
Thanks, Ajay
On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify. Thanks, Ajay Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used? Thanks, Ajay On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth. For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files. mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii 1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf? 2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial? Best, Ajay On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Doug, Thanks for the quick reply. Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis? Thanks, Ajay On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values). I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness. Thanks, Ajay On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Ok this makes more sense now. In my case if I choose abs I would look at the max cdf < 0.05 for the corresponding cluster extent in the TH13 folder.
In terms of the |a-b|<0,05 does this mean that if I got results in blue it just means significant but with no directionality as to if A > B or B>A? I guess with the blue and red color bars I thought directionality was implied.
Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in order to determine directionality of thickness results?
Thanks, Ajay
On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
Also is there a T/Z threshold applied? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?.
Thanks, Ajay
On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file.
In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail.
Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify.
Thanks, Ajay
Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo
On Friday, May 6, 2016, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used?
Thanks, Ajay
On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files.
mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii
- For cortical thickness does it make sense to use the --cortex option
or should I specify a mask of some type (if so which) in mris_surf2surf?
- For converting files to .gii should I be using rh.white as the
option or should it be rh.pial?
Best, Ajay
On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani dr.ajay.kurani@gmail.com wrote:
Hi Doug, Thanks for the quick reply.
Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis?
Thanks, Ajay
On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kurani@gmail.com
wrote:
Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values).
I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness.
Thanks, Ajay
On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kurani@gmail.com > wrote:
> Hi Freesurfer Experts, > I am trying to understand the difference between qcache option > and mris_fwhm and which is appropriate for a cortical thickness analysis. > I processed my files with qcache and have > lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool > SurfFWHM to estimate the smoothness of a subject at when looking at the > fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately > 9.3-9.9 smoothness level. > > I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i > lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when > using SurfFWHM on the smae subject the smoothness was estimated at 11.25. > > > 1) I am not sure if the qcache or the mris_fwhm file is more > appropriate to use for a cortical thickness analysis. > > 2) For qdec if I select the 15mm option does it assume the > smoothness is 15mm when calculating monte carlo corrections? Would there > be a different way to estimate this since my smoothness at 15mm is closer > to 10mm? > > Thanks, > Ajay >
The color still indicates the direction. If you have a signed hypothesis, then you can run it with pos or neg instead of abs, however, in this case it will change the voxel-wise cluster-forming threshold (make it more liberal) because the voxel-wise p-value is computed assuming an unsigned test.
On 05/10/2016 11:59 AM, Ajay Kurani wrote:
Hi Doug, Ok this makes more sense now. In my case if I choose abs I would look at the max cdf < 0.05 for the corresponding cluster extent in the TH13 folder.
In terms of the |a-b|<0,05 does this mean that if I got results in blue it just means significant but with no directionality as to if A > B or B>A? I guess with the blue and red color bars I thought directionality was implied.
Or would one need to do a subsequent one tailed test (Pos A>B; Neg B>A)d in order to determine directionality of thickness results?
Thanks, Ajay
On Mon, May 9, 2016 at 3:11 PM, Ajay Kurani <dr.ajay.kurani@gmail.com mailto:dr.ajay.kurani@gmail.com> wrote:
Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied? I initially thought that T or Z=1.3 is the threshold but in looking at tutorials I see that may be related to the color scale -log(0.05), so I am not sure if there is a minimum T/Z value to be included in the cluster or if I was correct at 1.3 is the threshold value (T or Z score or something else)?. Thanks, Ajay On Sun, May 8, 2016 at 7:33 PM, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Doug, Thanks for the explanation. In using p=0.05 with my thickness files (smoothed 15mm translates to FWHM=21mm), I looked at fwhm21/abs/th13/ cdf file. In regards to Qdec , if I choose abs, does the p=0.05/1.3 option mean the overall alpha (ie 2.5% for A>B, 2.5% for B>A ) or is it the alpha per tail (5% A>B, 5% B>A)? Would I look at the max cdf 0.05 which is a cluster size of 1302 or would I look at max cdf <0.1 which is 1109? This relates to the first question of if 0.05 relates to the overall probability or per tail. Also is there a T/Z threshold applied to these clusters or just cluster-extent is used? In looking at the tutorials I see that 1.3 really is -log(0.05) so I do not think this relates to any sort of T or Z threshold but I just wanted to verify. Thanks, Ajay Also, when smoothed at 15mm the estimated smoothness was around 21mm. When lo On Friday, May 6, 2016, Ajay Kurani <dr.ajay.kurani@gmail.com <mailto:dr.ajay.kurani@gmail.com>> wrote: Hi Doug, I wanted to figure out what is the minimum cluster extent for a given monte carlo simulation (ie when you choose p=0.5/T=1.3). I saw the following tutorial : https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo and so I wanted to know if freesurfer estimates the smoothness for each subject's cortical thickness for a hemisphere and then chooses the corresponding fwhm folder or if by choosing lh 15mm in qdec the clusterwise values are taken from the 15mm folder? Is the smoothness based on the smoothing kernel used or the inherent smoothness of that particular measure (ie measuring the smoothness of the input thicknesss image)? Is there a way to see what cluster minimum is used? Thanks, Ajay On Thu, May 5, 2016 at 3:49 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth. For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files. mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii 1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf? 2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial? Best, Ajay On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Doug, Thanks for the quick reply. Is there a difference from qcache/mris_fwhm with mris_smooth and mri_surf2surf -fwhm ? If so, which is recommended for cortical thickness analysis? Thanks, Ajay On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Freesurfer Experts, Just as a followup through my reading i've come across posts which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for smoothing. For my cortical thickness analysis I would like to smooth all of my rh/lh.thickness.fsaverage.mgh files for each subject in order to run a group analysis. After finding regions of difference, I would then like to use the ROI to extract each individual's mean thickness in the ROI in order to run a correlation with other measures. Based on this, I assume it would make sense to use smoothed data to identify the ROI and then use unsmoothed data for extracting actual thickness measures (does lh.thickness.fsaverage contain the original thickness or warped thickness values). I am unsure which smoothing is the most accurate or preferred. In using qcache the smoothness of the images do not seem to reach the filter level (based on the earlier email) so I am not sure if there is a freesurfer tool to check the smoothness level or if the qcache smoothness levels make sense for cortical thickness. Thanks, Ajay On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani <dr.ajay.kurani@gmail.com> wrote: Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25. 1) I am not sure if the qcache or the mris_fwhm file is more appropriate to use for a cortical thickness analysis. 2) For qdec if I select the 15mm option does it assume the smoothness is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm? Thanks, Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Underneath, they both use the same code, so they should give the same results. Are you saying they are different? I don't know what SurfFWHM is doing so I can't comment on what those results mean. Measuring the FWHM on the surface is quite tricky. doug
On 5/4/16 6:41 PM, Ajay Kurani wrote:
Hi Freesurfer Experts, I am trying to understand the difference between qcache option and mris_fwhm and which is appropriate for a cortical thickness analysis. I processed my files with qcache and have lh.thickness.fsaverage.fwhm15.gii (converted) files. I used an afni tool SurfFWHM to estimate the smoothness of a subject at when looking at the fwhm0 image it iwas 5.5 and for 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level.
I also used mris_fwhm --hemi lh --s fsaverage --smooth-only --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o test_15.gii and when using SurfFWHM on the smae subject the smoothness was estimated at 11.25.
- I am not sure if the qcache or the mris_fwhm file is more
appropriate to use for a cortical thickness analysis.
- For qdec if I select the 15mm option does it assume the smoothness
is 15mm when calculating monte carlo corrections? Would there be a different way to estimate this since my smoothness at 15mm is closer to 10mm?
Thanks, Ajay
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Ajay Kurani -
Douglas Greve -
Douglas N Greve